Summary
1. Here, I present a new, multifunctional phylogenetics package, phytools, for the R statistical computing environment.

2. The focus of the package is on methods for phylogenetic comparative biology; however, it also includes tools for tree inference, phylogeny input/output, plotting, manipulation and several other tasks.

3. I describe and tabulate the major methods implemented in phytools, and in addition provide some demonstration of its use in the form of two illustrative examples.

4. Finally, I conclude by briefly describing an active web-log that I use to document present and future developments for phytools. I also note other web resources for phylogenetics in the R computational environment.

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phytools: an R package for phylogenetic comparative biology (and other things)

Associations between modifiable exposures and disease seen in observational epidemiology are sometimes confounded and thus misleading, despite our best efforts to improve the design and analysis of studies. Mendelian randomization-the random assortment of genes from parents to offspring that occurs during gamete formation and conception-provides one method for assessing the causal nature of some environmental exposures. The association between a disease and a polymorphism that mimics the biological link between a proposed exposure and disease is not generally susceptible to the reverse causation or confounding that may distort interpretations of conventional observational studies. Several examples where the phenotypic effects of polymorphisms are well documented provide encouraging evidence of the explanatory power of Mendelian randomization and are described. The limitations of the approach include confounding by polymorphisms in linkage disequilibrium with the polymorphism under study, that polymorphisms may have several phenotypic effects associated with disease, the lack of suitable polymorphisms for studying modifiable exposures of interest, and canalization-the buffering of the effects of genetic variation during development. Nevertheless, Mendelian randomization provides new opportunities to test causality and demonstrates how investment in the human genome project may contribute to understanding and preventing the adverse effects on human health of modifiable exposures.

/pdf/mendelian-randomization-can-genetic-epidemiology-contribute-vb0zjyrtxf.pdf

‘Mendelian randomization’: can genetic epidemiology contribute to understanding environmental determinants of disease?

In recent months there has been an explosion of interest in using the Web to create, assemble, and disseminate geographic information provided voluntarily by individuals. Sites such as Wikimapia and OpenStreetMap are empowering citizens to create a global patchwork of geographic information, while Google Earth and other virtual globes are encouraging volunteers to develop inter- esting applications using their own data. I review this phenomenon, and examine associated issues: what drives people to do this, how accurate are the results, will they threaten individual privacy, and how can they augment more conventional sources? I compare this new phenomenon to more traditional citizen science and the role of the amateur in geographic observation.

/pdf/citizens-as-sensors-the-world-of-volunteered-geography-phibl484h3.pdf

Citizens as sensors: the world of volunteered geography

We review the recent rapid progress in the statistical physics of evolving networks. Interest has focused mainly on the structural properties of complex networks in communications, biology, social sciences and economics. A number of giant artificial networks of this kind have recently been created, which opens a wide field for the study of their topology, evolution, and the complex processes which occur in them. Such networks possess a rich set of scaling properties. A number of them are scale-free and show striking resilience against random breakdowns. In spite of the large sizes of these networks, the distances between most of their vertices are short - a feature known as the 'small-world' effect. We discuss how growing networks self-organize into scale-free structures, and investigate the role of the mechanism of preferential linking. We consider the topological and structural properties of evolving networks, and percolation and disease spread on these networks. We present a number of models demonstrat...

/pdf/evolution-of-networks-27h4ny8xbi.pdf

Evolution of networks

Yuelong Shu1, John McCauley2 1. WHO Collaborating Center for Reference and Research on Influenza, Chinese National Influenza Center, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China 2. WHO Collaborating Centre for Reference and Research on Influenza, Crick Worldwide Influenza Centre, the Francis Crick Institute, London, United Kingdom

GISAID: Global initiative on sharing all influenza data - from vision to reality.

an independent government advisory body on AIDS issues, last week urged prudence in implementing male-circumcision programmes to reduce the spread of HIV. It cautioned that over-zealous roll out could lead to a false sense of security and exacerbate the problem. In March, the World Health Organization (WHO) endorsed the promotion of male circumcision as a tool for HIV prevention, alongside condoms and antiretroviral drugs. The move was based on a WHO expert consultation, which concluded that the evidence for the intervention’s efficacy was “compelling”. Recent criticism of this view has been received with anger (see ‘Cutting criticism’). The strongest evidence comes from three recent studies. In 2005, a study of 3,300 heterosexual men living in and around Orange Farm, South Africa, by France’s National AIDS Research Agency, showed that circumcising men reduced the risk of infection by 60%. Similar levels of protection were found in 2007 by American-funded studies in Kisumu, Kenya, and Rakai, Uganda. Taken together with results from observational studies, this is “as convincing evidence as one ever gets in public health,” says Helen Weiss, a statistical epidemiologist at the London School of Hygiene & Tropical Medicine. But questions remain about the intervention’s applicability as a preventative tool on a large scale, says Willy Rozenbaum of the Pierre and Marie Curie University in Paris, who led the CNS study. Rozenbaum questions the speed with which the WHO has acted, and thinks the organization’s endorsement — although detailing the caveats — has been misunderstood in some quarters as saying circumcision is a “miracle solution”. Rozenbaum notes that the effect of circumcision on HIV prevalence in a population will depend on a host of social and cultural factors. There is a real risk, he says, that after circumcision men may have a false sense of security and increase their number of partners, or dispense with condoms. The report also points out that circumcision leaves men more vulnerable to Circumcision for HIV needs follow-up

Circumcision for HIV needs follow-up.

Thomson Reuters divests intellectual-property and science division in US$3.55-billion deal.

‘Web of Science’ to be sold to private-equity firms

Universities in France are set to receive an €11-billion (US$16-billion) windfall from a government initiative intended to create an ‘Ivy League’ of research centres. The cash could help to reverse the decades-long neglect of the country’s university system, although the bulk of the funding is likely to be channelled to just a few institutions. This would break a long-standing taboo in France, where the 83 previously centralized state universities have long been considered equal, at least in terms of government funding and researchers’ pay scales. The funding is part of a €35-billion package — the grand emprunt, or ‘big loan’ — announced by President Nicolas Sarkozy on 14 December, intended to boost the country’s long-term competitiveness. Borrowed mainly from international financial markets, the investment represents a hefty 1.8% of France’s annual gross domestic product, roughly equivalent in scale to the $53-billion science stimulus package announced earlier this year by the United States (see Nature 461, 856–857; 2009). Sarkozy’s spending priorities (see graphic) broadly follow recommendations made on 17 November by a blue-ribbon panel of researchers, industrialists and economists, and chaired by two former prime ministers, conservative Alain Juppé and socialist Michel Rocard. Panelist Edouard Bard, an oceanographer at the Paul-Cézanne University in Aix-Marseille, says he is pleased that Sarkozy heard the panel’s argument that increasing the international competiveness of France’s universities was the grand emprunt’s top priority. The funding should give universities the freedom and funding to attract talent from around the world by offering more competitive salaries and generous lab funding, he says.

/pdf/french-research-wins-huge-cash-boost-2za50wb7sr.pdf

Declan Butler

Papers

Circumcision for HIV needs follow-up.

‘Web of Science’ to be sold to private-equity firms

French research wins huge cash boost.

GlaxoSmithKline goes public with malaria data

Battle to boost the status of French universities